Even if some accommodation were made for pin-compatibility of the 3.3V <-> 5V for a given 5V shield, wouldn't there still be an issue with the shield actually requiring a SUPPLY-RAIL of 5V to be powered in the first place? How will the Arduino Due solve this problem -- is there a stepup converter, or else a 5V output LDO somewhere?

* 5V. This pin outputs a regulated 5V from the regulator on the board. The board can be supplied with power either from the DC power jack (7 - 12V), the USB connector (5V), or the VIN pin of the board (7-12V).